You use the following URL when logged into Google Webmaster Tools:

https://www.google.com/webmasters/tools/removals-request?hl=en&siteUrl=http://{YOUR_URL}/&urlt={URL_TO_BLOCK}

Then replace {YOUR_URL} with a URL you control within Webmaster Tools, and replace {URL_TO_BLOCK} with the URL of the site you want to block.

You could block a whole site, section or single page this way, based on how you entered the URL. To block a site, use the top level domain (E.g. http://www.someurl.com/), to block a section (subfolder) use a subfolder URL (E.g. http://www.someurl.com/somefolder/) and to block a page use the specific page URL (E.g. http://www.someurl.com/somefolder/somepage.html).

I am waiting an update from Google on why this happened, if site’s were impacted and how long this was an issue